[English] 日本語
Yorodumi
- EMDB-16549: structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16549
Titlestructure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome
Map dataLAFTER filtered
Sample
  • Complex: H3K36me3 dinucleosome-LEDGF/p75 PWWP domain complex
    • Complex: Histone
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H3
    • Complex: DNA
      • DNA: WIDOM 601 DNA
      • DNA: WIDOM 601 DNA
    • Complex: LEDGF/p75 PWWP domain complex
      • Protein or peptide: PC4 and SFRS1-interacting protein
Keywordsnucleosome / transcription activator / methylation / complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / mRNA 5'-splice site recognition / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin ...supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / mRNA 5'-splice site recognition / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / euchromatin / structural constituent of chromatin / nucleosome / nucleosome assembly / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Histone H2B signature. / Histone H2A conserved site ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3 / PC4 and SFRS1-interacting protein / Histone H2B 1.1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsKoutna E / Kouba T / Novacek J / Veverka V
Funding support Czech Republic, European Union, 3 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic22-03028S Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729European Union
Ministry of Education (MoE, Czech Republic)LO1304 Czech Republic
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Multivalency of nucleosome recognition by LEDGF.
Authors: Eliška Koutná / Vanda Lux / Tomáš Kouba / Jana Škerlová / Jiří Nováček / Pavel Srb / Rozálie Hexnerová / Hana Šváchová / Zdeněk Kukačka / Petr Novák / Milan Fábry / Simon ...Authors: Eliška Koutná / Vanda Lux / Tomáš Kouba / Jana Škerlová / Jiří Nováček / Pavel Srb / Rozálie Hexnerová / Hana Šváchová / Zdeněk Kukačka / Petr Novák / Milan Fábry / Simon Poepsel / Václav Veverka /
Abstract: Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription ...Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.
History
DepositionJan 25, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16549.png

Downloads & links

-
Map

FileDownload / File: emd_16549.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLAFTER filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 220 pix.
= 364.32 Å		1.66 Å/pix.
x 220 pix.
= 364.32 Å		1.66 Å/pix.
x 220 pix.
= 364.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.87772137 - 1.130135
Average (Standard dev.)0.0005756446 (±0.020611254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 364.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16549_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION post-processed

Fileemd_16549_additional_1.map
AnnotationRELION post-processed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16549_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16549_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : H3K36me3 dinucleosome-LEDGF/p75 PWWP domain complex

EntireName: H3K36me3 dinucleosome-LEDGF/p75 PWWP domain complex
Components
  • Complex: H3K36me3 dinucleosome-LEDGF/p75 PWWP domain complex
    • Complex: Histone
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H3
    • Complex: DNA
      • DNA: WIDOM 601 DNA
      • DNA: WIDOM 601 DNA
    • Complex: LEDGF/p75 PWWP domain complex
      • Protein or peptide: PC4 and SFRS1-interacting protein

+
Supramolecule #1: H3K36me3 dinucleosome-LEDGF/p75 PWWP domain complex

SupramoleculeName: H3K36me3 dinucleosome-LEDGF/p75 PWWP domain complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: H3K36me3 introduced by methyl-lysine analog method (methylated cystein as the pseudomethyl lysine)
Source (natural)Organism: Xenopus laevis (African clawed frog)

+
Supramolecule #2: Histone

SupramoleculeName: Histone / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #7
Source (natural)Organism: synthetic construct (others)

+
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: LEDGF/p75 PWWP domain complex

SupramoleculeName: LEDGF/p75 PWWP domain complex / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6

+
Macromolecule #1: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

+
Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

+
Macromolecule #3: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

+
Macromolecule #6: PC4 and SFRS1-interacting protein

MacromoleculeName: PC4 and SFRS1-interacting protein / type: protein_or_peptide / ID: 6
Details: DENSITY OF RESIDUE 30-34 AND RESIDUE 92-530 ARE INVISIBLE
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.224453 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTRDFKPGDL IFAKMKGYPH WPARVDEVPD GAVKPPTNKL PIFFFGTHET AFLGPKDIFP YSENKEKYGK PNKRKGFNEG LWEIDNNPK VKFSSQQAAT KQSNASSDVE VEEKETSVSK EDTDHEEKAS NEDVTKAVDI TTPKAARRGR KRKAEKQVET E EAGVVTTA ...String:
MTRDFKPGDL IFAKMKGYPH WPARVDEVPD GAVKPPTNKL PIFFFGTHET AFLGPKDIFP YSENKEKYGK PNKRKGFNEG LWEIDNNPK VKFSSQQAAT KQSNASSDVE VEEKETSVSK EDTDHEEKAS NEDVTKAVDI TTPKAARRGR KRKAEKQVET E EAGVVTTA TASVNLKVSP KRGRPAATEV KIPKPRGRPK MVKQPCPSES DIITEEDKSK KKGQEEKQPK KQPKKDEEGQ KE EDKPRKE PDKKEGKKEV ESKRKNLAKT GVTSTSDSEE EGDDQEGEKK RKGGRNFQTA HRRNMLKGQH EKEAADRKRK QEE QMETEQ QNKDEGKKPE VKKVEKKRET SMDSRLQRIH AEIKNSLKID NLDVNRCIEA LDELASLQVT MQQAQKHTEM ITTL KKIRR FKVSQVIMEK STMLYNKFKN MFLVGEGDSV ITQVLNKSLA EQRQHEEANK TKDQGKKGPN KKLEKEQTGS KTLNG GSDA QDGNQPQHNG ESNEDSKDNH EASTKKKPSS EERETEISLK DSTLDN

UniProtKB: PC4 and SFRS1-interacting protein

+
Macromolecule #7: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.331982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGV(ML3)KPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEASEAY LVALFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

+
Macromolecule #4: WIDOM 601 DNA

MacromoleculeName: WIDOM 601 DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 50.699316 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DC) (DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA) (DT)(DT)(DG)(DA)(DA)(DC)(DA) (DG)(DC) (DG)(DA)(DC)

+
Macromolecule #5: WIDOM 601 DNA

MacromoleculeName: WIDOM 601 DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.170602 KDa
SequenceString: (DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(DA) (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA) (DC)(DG)(DT)(DG)(DC)(DC) ...String:
(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(DA) (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT) (DG)(DA)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49681
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3mvd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8cbq:
structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more